Electronic medical record systems, data quality and loss to follow-up: survey of antiretroviral therapy programmes in resource-limited settings

OBJECTIVE: To describe the electronic medical databases used in antiretroviral therapy (ART) programmes in lower-income countries and assess the measures such programmes employ to maintain and improve data quality and reduce the loss of patients to follow-up. METHODS: In 15 countries of Africa, South America and Asia, a survey was conducted from December 2006 to February 2007 on the use of electronic medical record systems in ART programmes. Patients enrolled in the sites at the time of the survey but not seen during the previous 12 months were considered lost to follow-up. The quality of the data was assessed by computing the percentage of missing key variables (age, sex, clinical stage of HIV infection, CD4+ lymphocyte count and year of ART initiation). Associations between site characteristics (such as number of staff members dedicated to data management), measures to reduce loss to follow-up (such as the presence of staff dedicated to tracing patients) and data quality and loss to follow-up were analysed using multivariate logit models. FINDINGS: Twenty-one sites that together provided ART to 50 060 patients were included (median number of patients per site: 1000; interquartile range, IQR: 72-19 320). Eighteen sites (86%) used an electronic database for medical record-keeping; 15 (83%) such sites relied on software intended for personal or small business use. The median percentage of missing data for key variables per site was 10.9% (IQR: 2.0-18.9%) and declined with training in data management (odds ratio, OR: 0.58; 95% confidence interval, CI: 0.37-0.90) and weekly hours spent by a clerk on the database per 100 patients on ART (OR: 0.95; 95% CI: 0.90-0.99). About 10 weekly hours per 100 patients on ART were required to reduce missing data for key variables to below 10%. The median percentage of patients lost to follow-up 1 year after starting ART was 8.5% (IQR: 4.2-19.7%). Strategies to reduce loss to follow-up included outreach teams, community-based organizations and checking death registry data. Implementation of all three strategies substantially reduced losses to follow-up (OR: 0.17; 95% CI: 0.15-0.20). CONCLUSION: The quality of the data collected and the retention of patients in ART treatment programmes are unsatisfactory for many sites involved in the scale-up of ART in resource-limited settings, mainly because of insufficient staff trained to manage data and trace patients lost to follow-up.

Gender and the use of antiretroviral treatment in resource-constrained settings: findings from a multicenter collaboration

AIMS: To compare the gender distribution of HIV-infected adults receiving highly active antiretroviral treatment (HAART) in resource-constrained settings with estimates of the gender distribution of HIV infection; to describe the clinical characteristics of women and men receiving HAART. METHODS: The Antiretroviral Therapy in Lower-Income Countries, ART-LINC Collaboration is a network of clinics providing HAART in Africa, Latin America, and Asia. We compared UNAIDS data on the gender distribution of HIV infection with the proportions of women and men receiving HAART in the ART-LINC Collaboration. RESULTS: Twenty-nine centers in 13 countries participated. Among 33,164 individuals, 19,989 (60.3%) were women. Proportions of women receiving HAART in ART-LINC centers were similar to, or higher than, UNAIDS estimates of the proportions of HIV-infected women in all but two centers. There were fewer women receiving HAART than expected from UNAIDS data in one center in Uganda and one center in India. Taking into account heterogeneity across cohorts, women were younger than men, less likely to have advanced HIV infection, and more likely to be anemic at HAART initiation. CONCLUSIONS: Women in resource-constrained settings are not necessarily disadvantaged in their access to HAART. More attention needs to be paid to ensuring that HIV-infected men are seeking care and starting HAART.

Mortality of patients lost to follow-up in antiretroviral treatment programmes in resource-limited settings: systematic review and meta-analysis

BACKGROUND: The retention of patients in antiretroviral therapy (ART) programmes is an important issue in resource-limited settings. Loss to follow up can be substantial, but it is unclear what the outcomes are in patients who are lost to programmes. METHODS AND FINDINGS: We searched the PubMed, EMBASE, Latin American and Caribbean Health Sciences Literature (LILACS), Indian Medlars Centre (IndMed) and African Index Medicus (AIM) databases and the abstracts of three conferences for studies that traced patients lost to follow up to ascertain their vital status. Main outcomes were the proportion of patients traced, the proportion found to be alive and the proportion that had died. Where available, we also examined the reasons why some patients could not be traced, why patients found to be alive did not return to the clinic, and the causes of death. We combined mortality data from several studies using random-effects meta-analysis. Seventeen studies were eligible. All were from sub-Saharan Africa, except one study from India, and none were conducted in children. A total of 6420 patients (range 44 to 1343 patients) were included. Patients were traced using telephone calls, home visits and through social networks. Overall the vital status of 4021 patients could be ascertained (63%, range across studies: 45% to 86%); 1602 patients had died. The combined mortality was 40% (95% confidence interval 33%-48%), with substantial heterogeneity between studies (P<0.0001). Mortality in African programmes ranged from 12% to 87% of patients lost to follow-up. Mortality was inversely associated with the rate of loss to follow up in the programme: it declined from around 60% to 20% as the percentage of patients lost to the programme increased from 5% to 50%. Among patients not found, telephone numbers and addresses were frequently incorrect or missing. Common reasons for not returning to the clinic were transfer to another programme, financial problems and improving or deteriorating health. Causes of death were available for 47 deaths: 29 (62%) died of an AIDS defining illness. CONCLUSIONS: In ART programmes in resource-limited settings a substantial minority of adults lost to follow up cannot be traced, and among those traced 20% to 60% had died. Our findings have implications both for patient care and the monitoring and evaluation of programmes.

Switching to second-line antiretroviral therapy in resource-limited settings: comparison of programmes with and without viral load monitoring

BACKGROUND: In high-income countries, viral load is routinely measured to detect failure of antiretroviral therapy (ART) and guide switching to second-line ART. Viral load monitoring is not generally available in resource-limited settings. We examined switching from nonnucleoside reverse transcriptase inhibitor (NNRTI)-based first-line regimens to protease inhibitor-based regimens in Africa, South America and Asia. DESIGN AND METHODS: Multicohort study of 17 ART programmes. All sites monitored CD4 cell count and had access to second-line ART and 10 sites monitored viral load. We compared times to switching, CD4 cell counts at switching and obtained adjusted hazard ratios for switching (aHRs) with 95% confidence intervals (CIs) from random-effects Weibull models. RESULTS: A total of 20 113 patients, including 6369 (31.7%) patients from 10 programmes with access to viral load monitoring, were analysed; 576 patients (2.9%) switched. Low CD4 cell counts at ART initiation were associated with switching in all programmes. Median time to switching was 16.3 months [interquartile range (IQR) 10.1-26.6] in programmes with viral load monitoring and 21.8 months (IQR 14.0-21.8) in programmes without viral load monitoring (P < 0.001). Median CD4 cell counts at switching were 161 cells/microl (IQR 77-265) in programmes with viral load monitoring and 102 cells/microl (44-181) in programmes without viral load monitoring (P < 0.001). Switching was more common in programmes with viral load monitoring during months 7-18 after starting ART (aHR 1.38; 95% CI 0.97-1.98), similar during months 19-30 (aHR 0.97; 95% CI 0.58-1.60) and less common during months 31-42 (aHR 0.29; 95% CI 0.11-0.79). CONCLUSION: In resource-limited settings, switching to second-line regimens tends to occur earlier and at higher CD4 cell counts in ART programmes with viral load monitoring compared with programmes without viral load monitoring.

Is differentiation of frequently encountered foreign bodies in corpses possible by Hounsfield density measurement?

The radiological determination of foreign objects in corpses can be difficult if they are fragmented or deformed. With multislice computed tomography, radiodensities--referred to as Hounsfield units (HU)--can be measured. We examined the possibility of differentiating 21 frequently occurring foreign bodies, such as metals, rocks, and different manmade materials by virtue of their HU values. Gold, steel, and brass showed mean HU values of 30671-30710 (upper measurable limit), mean HU values for steel, silver, copper, and limestone were 20346, 16949, 14033, and 2765, respectively. The group consisting of objects, such as aluminum, tarmac, car front-window glass, and other rocks, displayed mean HU values of 2329-2131 HU. The mean HU value of bottle glass and car side-window glass was 2088, whereas windowpane glass was 493. HU value determination may therefore help in preautopsy differentiation between case-relevant and irrelevant foreign bodies and thus be useful for autopsy planning and extraction of the objects in question.

Practical Object-Oriented Back-in-Time Debugging

Back-in-time debuggers are extremely useful tools for identifying the causes of bugs, as they allow us to inspect the past states of objects no longer present in the current execution stack. Unfortunately the "omniscient" approaches that try to remember all previous states are impractical because they either consume too much space or they are far too slow. Several approaches rely on heuristics to limit these penalties, but they ultimately end up throwing out too much relevant information. In this paper we propose a practical approach to back-in-time debugging that attempts to keep track of only the relevant past data. In contrast to other approaches, we keep object history information together with the regular objects in the application memory. Although seemingly counter-intuitive, this approach has the effect that past data that is not reachable from current application objects (and hence, no longer relevant) is automatically garbage collected. In this paper we describe the technical details of our approach, and we present benchmarks that demonstrate that memory consumption stays within practical bounds. Furthermore since our approach works at the virtual machine level, the performance penalty is significantly better than with other approaches.

Flow-Centric, Back-In-Time Debugging

Conventional debugging tools present developers with means to explore the run-time context in which an error has occurred. In many cases this is enough to help the developer discover the faulty source code and correct it. However, rather often errors occur due to code that has executed in the past, leaving certain objects in an inconsistent state. The actual run-time error only occurs when these inconsistent objects are used later in the program. So-called back-in-time debuggers help developers step back through earlier states of the program and explore execution contexts not available to conventional debuggers. Nevertheless, even back-in-time debuggers do not help answer the question, ``Where did this object come from?'' The Object-Flow Virtual Machine, which we have proposed in previous work, tracks the flow of objects to answer precisely such questions, but this VM does not provide dedicated debugging support to explore faulty programs. In this paper we present a novel debugger, called Compass, to navigate between conventional run-time stack-oriented control flow views and object flows. Compass enables a developer to effectively navigate from an object contributing to an error back-in-time through all the code that has touched the object. We present the design and implementation of Compass, and we demonstrate how flow-centric, back-in-time debugging can be used to effectively locate the source of hard-to-find bugs.

A Calculus of Evolving Objects

The demands of developing modern, highly dynamic applications have led to an increasing interest in dynamic programming languages and mechanisms. Not only applications must evolve over time, but the object models themselves may need to be adapted to the requirements of different run-time contexts. Class-based models and prototype-based models, for example, may need to co-exist to meet the demands of dynamically evolving applications. Multi-dimensional dispatch, fine-grained and dynamic software composition, and run-time evolution of behaviour are further examples of diverse mechanisms which may need to co-exist in a dynamically evolving run-time environment How can we model the semantics of these highly dynamic features, yet still offer some reasonable safety guarantees? To this end we present an original calculus in which objects can adapt their behaviour at run-time to changing contexts. Both objects and environments are represented by first-class mappings between variables and values. Message sends are dynamically resolved to method calls. Variables may be dynamically bound, making it possible to model a variety of dynamic mechanisms within the same calculus. Despite the highly dynamic nature of the calculus, safety properties are assured by a type assignment system.

Tuberculosis in antiretroviral treatment programs in lower income countries: availability and use of diagnostics and screening

OBJECTIVES In resource-constrained settings, tuberculosis (TB) is a common opportunistic infection and cause of death in HIV-infected persons. TB may be present at the start of antiretroviral therapy (ART), but it is often under-diagnosed. We describe approaches to TB diagnosis and screening of TB in ART programs in low- and middle-income countries. METHODS AND FINDINGS We surveyed ART programs treating HIV-infected adults in sub-Saharan Africa, Asia and Latin America in 2012 using online questionnaires to collect program-level and patient-level data. Forty-seven sites from 26 countries participated. Patient-level data were collected on 987 adult TB patients from 40 sites (median age 34.7 years; 54% female). Sputum smear microscopy and chest radiograph were available in 47 (100%) sites, TB culture in 44 (94%), and Xpert MTB/RIF in 23 (49%). Xpert MTB/RIF was rarely available in Central Africa and South America. In sites with access to these diagnostics, microscopy was used in 745 (76%) patients diagnosed with TB, culture in 220 (24%), and chest X-ray in 688 (70%) patients. When free of charge culture was done in 27% of patients, compared to 21% when there was a fee (p = 0.033). Corresponding percentages for Xpert MTB/RIF were 26% and 15% of patients (p = 0.001). Screening practices for active disease before starting ART included symptom screening (46 sites, 98%), chest X-ray (38, 81%), sputum microscopy (37, 79%), culture (16, 34%), and Xpert MTB/RIF (5, 11%). CONCLUSIONS Mycobacterial culture was infrequently used despite its availability at most sites, while Xpert MTB/RIF was not generally available. Use of available diagnostics was higher when offered free of charge.

REE and Hf distribution among mineral phases in the CV-CK clan : a way to explain present-day Hf isotopic variations in chondrites

Chondrites are among the most primitive objects in the Solar System and constitute the main building blocks of telluric planets. Among the radiochronometers currently used for dating geological events, Sm–Nd and Lu–Hf are both composed of refractory, lithophile element. They are thought to behave similarly as the parent elements (Sm and Lu) are generally less incompatible than the daughter elements (Nd and Hf) during geological processes. As such, their respective average isotopic compositions for the solar system should be well defined by the average of chondrites, called Chondritic Uniform Reservoir (CHUR). However, while the Sm–Nd isotopic system shows an actual spread of less than 4% in the average chondritic record, the Lu–Hf system shows a larger variation range of 28% [Bouvier A., Vervoort J. D. and Patchett P. J. (2008) The Lu–Hf and Sm–Nd isotopic composition of CHUR: Constraints from unequilibrated chondrites and implications for the bulk composition of terrestrial planets. Earth Planet. Sci. Lett.273, 48–57]. To better understand the contrast between Sm–Nd and Lu–Hf systems, the REE and Hf distribution among mineral phases during metamorphism of Karoonda (CK) and Vigarano-type (CV) carbonaceous chondrites has been examined. Mineral modes were determined from elemental mapping on a set of five CK chondrites (from types 3–6) and one CV3 chondrite. Trace-element patterns are obtained for the first time in all the chondrite-forming minerals of a given class (CK chondrites) as well as one CV3 sample. This study reveals that REE are distributed among both phosphates and silicates. Only 30–50% of Sm and Nd are stored in phosphates (at least in chondrites types 3–5); as such, they are not mobilized during early stages of metamorphism. The remaining fraction of Sm and Nd is distributed among the same mineral phases; these elements are therefore not decoupled during metamorphism. Of the whole-rock total of Lu, the fraction held in phosphate decreases significantly as the degree of metamorphism increases (30% for types 3 and 4, less than 5% in type 6). In contrast to Lu, Hf is mainly hosted by silicates with little contribution from phosphates throughout the CK metamorphic sequence. A significant part of Sm and Nd are stored in phosphates in types 3–5, and these elements behave similarly during CK chondrite metamorphism. That explains the robustness of the Sm/Nd ratios in chondrites through metamorphism, and the slight discrepancies observed in the present-day isotopic Nd values in chondrites. On the contrary, Lu and Hf are borne by several different minerals and consequently they are redistributed during metamorphism–induced recrystallization. The Lu/Hf ratios are therefore significantly disturbed during chondrites metamorphism, leading to the high discrepancies observed in present-day Hf isotopic values in chondrites.

The Forensic Reference Phantom-a new tool for quality assurance of attenuation measurements in forensic radiology

Introduction The purpose of this paper is to present the technical specifications of the Forensic Reference Phantom (FRP), to test its behavior relative to organic test materials, and discuss potential applications of the phantom in forensic radiology. Materials and method The FRP prototype is made of synthetic materials designed to simulate the computed tomography (CT) attenuation of water. It has six bore holes that accommodate multiuse containers. These containers were filled with test materials and scanned at 80 kVp, 120 kVp, and 140 kVp. X-ray attenuation was measured by two readers. Intra- and inter-reader reliability was assessed using the intra-class correlation coefficient (ICC). Significance levels between mean CT numbers at 80 kVp, 120 kVp, and 140 kVp were assessed with the Friedman-test. The T-test was used to assess significance levels between the FRP and water. Results Overall mean CT numbers ranged from −3.0–3.7HU for the FRP; −1000.3–−993.5HU for air; −157.7– −108.1HU for oil; 35.5–42.0HU for musle tissue; and 1301.5–2354.8HU for cortical bone. Inter-reader and intra-reader reliability were excellent (ICC>0.994; and ICC=0.999 respectively). CT numbers were significantly different at different energy levels. There was no significant difference between the attenuation of the FRP and water. Conclusions The FRP is a new tool for quality assurance and research in forensic radiology. The mean CT attenuation of the FRP is equivalent to water. The phantom can be scanned during routine post-mortem CT to assess the composition of unidentified objects. In addition, the FRP may be used to investigate new imaging algorithms and scan protocols in forensic radiology.

Limited clinical benefit of minority K103N and Y181C-variant detection in addition to routine genotypic resistance testing in antiretroviral therapy-naive patients

OBJECTIVE: The presence of minority nonnucleoside reverse transcriptase inhibitor (NNRTI)-resistant HIV-1 variants prior to antiretroviral therapy (ART) has been linked to virologic failure in treatment-naive patients. DESIGN: We performed a large retrospective study to determine the number of treatment failures that could have been prevented by implementing minority drug-resistant HIV-1 variant analyses in ART-naïve patients in whom no NNRTI resistance mutations were detected by routine resistance testing. METHODS: Of 1608 patients in the Swiss HIV Cohort Study, who have initiated first-line ART with two nucleoside reverse transcriptase inhibitors (NRTIs) and one NNRTI before July 2008, 519 patients were eligible by means of HIV-1 subtype, viral load and sample availability. Key NNRTI drug resistance mutations K103N and Y181C were measured by allele-specific PCR in 208 of 519 randomly chosen patients. RESULTS: Minority K103N and Y181C drug resistance mutations were detected in five out of 190 (2.6%) and 10 out of 201 (5%) patients, respectively. Focusing on 183 patients for whom virologic success or failure could be examined, virologic failure occurred in seven out of 183 (3.8%) patients; minority K103N and/or Y181C variants were present prior to ART initiation in only two of those patients. The NNRTI-containing, first-line ART was effective in 10 patients with preexisting minority NNRTI-resistant HIV-1 variant. CONCLUSION: As revealed in settings of case-control studies, minority NNRTI-resistant HIV-1 variants can have an impact on ART. However, the sole implementation of minority NNRTI-resistant HIV-1 variant analysis in addition to genotypic resistance testing (GRT) cannot be recommended in routine clinical settings. Additional associated risk factors need to be discovered.

Hierarchical self-assembly of nucleotide-appended oligopyrenotides into defined supramolecular objects

Supramolecular DNA assembly blends DNA building blocks with synthetic organic and inorganic molecules giving structural and functional advantages both to the initial self-assembly process and to the final construct. Synthetic molecules can bring a number of additional interactions into DNA nanotechnology. Incorporating extended aromatic molecules as connectors of DNA strands allows folding of these strands through π-π stacking (DNA “foldamers”). In previous work it was shown that short oligopyrenotides (phosphodiester-linked pyrene oligomers) behave as staircase-like foldamers, which cooperatively self-assemble into two-dimensional supramolecular polymers in aqueous medium. Herein, we demonstrate that a 10-mer DNA-sequence modified with 7 pyrene units (see illustration) forms dimensionally-defined supramolecular polymers under thermodynamic conditions in water. We present the self-assembly behavior, morphological studies, and the spectroscopic properties of the investigated DNA-sequences (illustrative AFM picture shown below).